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O₂ Migration Pathways Are Not Conserved across Proteins of a Similar Fold

Beckman Institute, University of Illinois, Urbana, Illinois

Correspondence: Address reprint requests to Klaus Schulten, Beckman Institute, University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801. Tel.: 217-244-1604; Fax: 217-244-6078; E-mail: kschulte{at}ks.uiuc.edu.

Recent advances in computational biology have made it possible to map the complete network and energy profile of gas migration pathways inside proteins. Although networks of O₂ pathways have already been characterized for a small number of proteins, the general properties and locations of these pathways have not been previously compared between proteins. In this study, maps of the O₂ pathways inside 12 monomeric globins were computed. It is found that, despite the conserved tertiary structure fold of the studied globins, the shape and topology of O₂ pathway networks exhibit a large variability between different globins, except when two globins are nearly identical. The locations of the O₂ pathways are, however, found to be correlated with the location of large hydrophobic residues, and a similar correlation is observed in two unrelated protein families: monomeric globins and copper-containing amine oxidases. The results have implications for the evolution of gas pathways in proteins and for protein engineering applications involving modifications of these pathways.